Really don't know the answer but to me, if the baffle design was identical, a larger exit pipe would produce a lower frequency exhaust tone/note than a smaller exit pipe would. Since our ears perceive lower frequencies to be lower in db or sound pressure, I would say the 3.5" would appear louder but only in db. (maybe ?)
Now that is based on identical baffles which I am sure they are not.
Good question.. I am sure others will chime in.